Available student project - Protein structure: new topological methods

Research fields

  • Biophysics
  • Topological and Structural Science

Project details

We prefer to ignore the usual motifs of protein secondary and higher structure, and search for an alternative, robust measure of structure. One ("contact map") approach that we have developed involved measuring effective networks of graphs whose nodes are alpha carbons in the protein chain, and whose edges link nodes within a certain effective distance. This approach, for certain distances, allows sensitive detection of the interior and the surface of a protein. Can we use it to classify different proteins? Preliminary results suggest we can, and further work is needed to develop this idea, using other tools of graph theory, such as graph spectra. Directions for a project could include

  1. classification of proteins whose conventional folds are considered to be close to "unstructured"
  2. surface to colume characterisation of biologically related proteins
  3. relations between contact maps and 2D NMR characterisation of proteins

Required background

No specialised background is needed. Interest and curiosity in application of basic concepts of structure, protein folding and graph theory is essential.

Project suitability

This research project can be tailored to suit students of the following type(s)
  • Honours project
  • Phd or Masters

Contact supervisor

Hyde, Stephen profile

Updated:  17 August 2017/ Responsible Officer:  Director, RSPE/ Page Contact:  Physics Webmaster